In [6]:
p1
set.seed(2021)
suppressMessages(library(ArchR))
addArchRThreads(threads = 16)
s <- function(x, pattern, slot = 1, ...) {
sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
Warning message: “package ‘ArchR’ was built under R version 4.1.2” Setting default number of Parallel threads to 16.
markerGenePlot <- function(proj, genes ) {
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = genes, embedding = "UMAPH230", imputeWeights = NULL)
p3 <- lapply(p, function(x){
x + guides(color = 'none', fill = 'none') +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
}
options(stringsAsFactors = F)
options(repr.plot.width=11, repr.plot.height=8.5)
# path to archr project
ARCHDIR = '/projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchR_Seal001_MJL'
PROJDIR = '/projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data'
### load rheMac10 ArchR genome ###
GENOMEDIR = '/home/bnphan/resources/genomes/rheMac10'
load(file.path(GENOMEDIR,'rheMac10_liftoff_GRCh38.p13_ArchR_annotations.rda'))
proj = loadArchRProject(ARCHDIR)
# Get names of available genes
genes <- getFeatures(
ArchRProj = proj,
useMatrix = "GeneScoreMatrix",
select = NULL,
ignoreCase = TRUE
)
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
proj
table(proj$Celltype1)
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchR_Seal001_MJL samples(5): DH-1_SEA1346A1 DH-3_SEA1346A3 DH-4_SEA1346A4 DH-5_SEA1346A5 DH-2_SEA1346A2 sampleColData names(1): ArrowFiles cellColData names(26): Sample TSSEnrichment ... ClustersI230 ClustersH230 numberOfCells(1): 43829 medianTSS(1): 24.36 medianFrags(1): 12627
< table of extent 0 >
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersH230", embedding = "UMAPH230")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2bae0bcbdc-Date-2022-04-11_Time-12-28-04.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2bae0bcbdc-Date-2022-04-11_Time-12-28-04.log
p1
# Andreas's final categories of neuron subtypes
# mac2mmfamD = {};
# mac2mmfamD['GLUT1'] = 'Ex-Reln';
# mac2mmfamD['GLUT2'] = 'Ex-Reln';
# mac2mmfamD['GLUT3'] = 'Ex-Sox5';
# mac2mmfamD['GLUT4'] = 'Ex-Sox5';
# mac2mmfamD['GLUT5'] = 'Ex-Sox5';
# mac2mmfamD['GLUT6'] = 'Ex-Sox5';
# mac2mmfamD['GLUT7'] = 'Ex-Maf';
# mac2mmfamD['GLUT8'] = 'Ex-Cpne3';
# mac2mmfamD['GLUT9'] = 'Ex-Prkcg';
# mac2mmfamD['GLUT10'] = 'Ex-Prkcg';
# mac2mmfamD['GLUT11'] = 'Ex-Rreb1';
# mac2mmfamD['GABA1'] = 'Inh-Cdh3';
# mac2mmfamD['GABA2_1'] = 'Inh-Rorb';
# mac2mmfamD['GABA2_2'] = 'Inh-Adamts5';
# mac2mmfamD['GABA3'] = 'Inh-Npy';
# mac2mmfamD['GABA4_1'] = 'Inh-Rorb';
# mac2mmfamD['GABA4_2'] = 'Inh-Adamts5';
# mac2mmfamD['GABA5'] = 'Inh-Pdyn';
# mac2mmfamD['midVen'] = 'midVent';
### Using Andreas's gene choices, visualize clusters based on gene expression
### How I found gene names: genes[startsWith(genes,'MAF')] <- example
### Excitatory neurons
markEx = c('RELN','SOX5','MAF', 'CPNE4', 'PRKCG',
'RREB1')
# name = Ensembl-v instead of markMSN3
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markEx, embedding = "UMAPH230", imputeWeights = NULL)
p_ex <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
#do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1a8648d02bac-Date-2022-04-10_Time-12-33-09.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-10 12:33:10 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1a8648d02bac-Date-2022-04-10_Time-12-33-09.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
do.call(cowplot::plot_grid, c(list(ncol = 3),p_ex))
### Inhibitory neurons
markInh = c('CDH3','RORB','ADAMTS5','NPY', 'PDYN')
# name = Ensembl-v instead of markMSN3
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markInh, embedding = "UMAPH230", imputeWeights = NULL)
p_inh <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1a86474ec80f4-Date-2022-04-10_Time-12-34-47.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-10 12:34:48 : Plotting Embedding 1 2 3 4 5 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1a86474ec80f4-Date-2022-04-10_Time-12-34-47.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
do.call(cowplot::plot_grid, c(list(ncol = 3),p_inh))
###### Dorsal Horn Atlas Nature Neuro Marker Genes
###### NN: Nature Neuro
###### Inhibitory
markInh_NN = c('SLC32A1', # GABA transporter Vgat
'GAD1',
'GAD2')
markerGenePlot(proj, markInh_NN)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-66d6b75db516f-Date-2022-04-07_Time-13-05-15.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-07 13:05:15 : Plotting Embedding 1 2 3 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-66d6b75db516f-Date-2022-04-07_Time-13-05-15.log
###### Dorsal Horn Atlas Nature Neuro Marker Genes
###### NN: Nature Neuro
###### Excitatory
options(repr.plot.width=11, repr.plot.height=8.5)
genes[startsWith(genes,'Cacnad1')]
#not found: 'CACNAD1'
markEx_NN = c('SLC17A6',# Glu transporter Vglu2
'NRN1'
)
markerGenePlot(proj, markEx_NN)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-66d6b7dbd2d43-Date-2022-04-07_Time-13-05-55.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-07 13:05:55 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-66d6b7dbd2d43-Date-2022-04-07_Time-13-05-55.log
###### Dorsal Horn Atlas Nature Neuro Marker Genes
###### NN: Nature Neuro
###### Excitatory
options(repr.plot.width=11, repr.plot.height=40)
#### DETAILED CELL TYPES
genes[startsWith(genes,'Cacnad1')]
#not found: NFATC1,ECI3,TAC2
markEx_NN_fig1b = c('SLC17A6', 'CRABP1', 'SPP1', 'SH3BGR', 'HTR1A' ,'KRT25', 'RXFP2', 'EYA2', 'TAC1',
'CHRM3','ACAP1', 'BMP7','SPON1' ,'QRFPR', 'CDH9', 'DUSP12',
'LGALS9', 'GAL', 'PNOC', 'TSEN54','TACR1', 'CRH',
'LMO4', 'NTNG1', 'NEFM', 'GDA', 'ADRA2A', 'LMO3',
'GPR101', 'RELN', 'COL11A1', 'NMUR2', 'NMU', 'PTHLH',
'UCN3', 'CBLN2', 'CPNE4', 'PLCH2', 'CLDN1')
markerGenePlot(proj, markEx_NN_fig1b)
options(repr.plot.width=11, repr.plot.height=8.5)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-66d6b47f103bd-Date-2022-04-07_Time-13-06-06.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-07 13:06:07 : Plotting Embedding 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-66d6b47f103bd-Date-2022-04-07_Time-13-06-06.log
################### Inhibitory - detailed
#### Not found: '2010001M06RIK', 'C530044C16RIK', 'GM20754', 'GM2694'
markInh_NN_fig1b = c('SLC32A1', 'HTR3A' ,'AQP6','SEMA3E' ,'SLC30A3','TfAP2B','NR2F2',
'GPC5','ID2','ADAMTS5', 'FRZB','CHRDL1','KRT17',
'NPY','TRHR','ECEL1',
'ADAMTSL2','PDYN','SSTR1','CRYM','HLCS' ,
'LYPD1','POU4F1' ,'MEIS2' ,'GRPR','COL5A2','MYO5B',
'CBLN4','BDNF','SOSTDC1' ,'NPFF' ,
'SMOC2' ,'GRP','LRRC38' ,'NTS' ,'TRH','CCK',
'MAF','NRN1')
options(repr.plot.width=11, repr.plot.height=40)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markInh_NN_fig1b, embedding = "UMAPH230", imputeWeights = NULL)
p3 <- lapply(p, function(x){
x + guides(color = "none", fill = "none") +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
options(repr.plot.width=11, repr.plot.height=8.5)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-66d6b7cd4aa6c-Date-2022-04-07_Time-13-07-47.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-07 13:07:48 : Plotting Embedding 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-66d6b7cd4aa6c-Date-2022-04-07_Time-13-07-47.log
##### Astrocyte 1 & 2 - based on Michael's rna-seq figure
markAstro1 = c('GFAP', 'GFAP') # not found: 'TGB4'
markAstro2 = c('SLC7A10', 'TRPM3', 'PDZRN4', 'MFGE8')
markerGenePlot(proj, markAstro1)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba38bd41cd-Date-2022-04-11_Time-12-28-19.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:28:20 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba38bd41cd-Date-2022-04-11_Time-12-28-19.log
markerGenePlot(proj, markAstro2)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba549e4a40-Date-2022-04-11_Time-12-28-33.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:28:34 : Plotting Embedding 1 2 3 4 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba549e4a40-Date-2022-04-11_Time-12-28-33.log
##### Ependymal- - based on Michael's rna-seq figure
markEpendymal = c('RFX2', 'DNAH12')
markerGenePlot(proj, markEpendymal)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba3acde93c-Date-2022-04-11_Time-12-28-52.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:28:53 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba3acde93c-Date-2022-04-11_Time-12-28-52.log
##### Meninges- - based on Michael's rna-seq figure
markMeninges = c('LAMA2', 'BICC1')
markerGenePlot(proj, markMeninges)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba4f6a3e81-Date-2022-04-11_Time-12-29-03.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:29:04 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba4f6a3e81-Date-2022-04-11_Time-12-29-03.log
##### Meninges- - based on search
#### https://www.biorxiv.org/content/10.1101/648642v1.full.pdf
markMeninges_search = c('FOXC1', 'S100A6', 'CRABP2', 'CRYM')
markerGenePlot(proj, markMeninges_search)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba6239459a-Date-2022-04-11_Time-12-29-14.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:29:15 : Plotting Embedding 1 2 3 4 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba6239459a-Date-2022-04-11_Time-12-29-14.log
##### microglia - - based on Michael's rna-seq figure
markMicroglia = c('MYO1F', 'PALD1')
markerGenePlot(proj, markMicroglia)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba5300c50-Date-2022-04-11_Time-12-29-33.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:29:34 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba5300c50-Date-2022-04-11_Time-12-29-33.log
##### Neurons - - based on Michael's rna-seq figure
markNeurons = c('SRRM3', 'MYT1L', 'RBFOX3')
markerGenePlot(proj, markNeurons)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba2894cd6c-Date-2022-04-11_Time-12-29-44.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:29:45 : Plotting Embedding 1 2 3 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba2894cd6c-Date-2022-04-11_Time-12-29-44.log
##### OPCs - - based on Michael's rna-seq figure
markOPCs = c('MEGF11', 'UST', 'TNR')
# from BaDoi: PDGFA (transcription factor)
markerGenePlot(proj, markOPCs)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba37117c9a-Date-2022-04-11_Time-12-30-00.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:30:00 : Plotting Embedding 1 2 3 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba37117c9a-Date-2022-04-11_Time-12-30-00.log
##### Oligos 1 and 2 - - based on Michael's rna-seq figure
markOligo1 = c('QDPR', 'QDPR')
markerGenePlot(proj, markOligo1)
#From Badoi : MOG
#MAG
#MBP
markOligo_BaDoi = c('MAG', 'MBP')
markerGenePlot(proj, markOligo_BaDoi)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba622fa902-Date-2022-04-11_Time-12-30-21.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:30:22 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba622fa902-Date-2022-04-11_Time-12-30-21.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba471976a9-Date-2022-04-11_Time-12-30-28.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:30:29 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba471976a9-Date-2022-04-11_Time-12-30-28.log
markOligo2 = c('DPY19L1', 'DPY19L1') # not found: 'S100B'
markerGenePlot(proj, markOligo2)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2baa32904c-Date-2022-04-11_Time-12-30-38.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:30:38 : Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2baa32904c-Date-2022-04-11_Time-12-30-38.log
markSchwann = c('UST', 'MPZ', 'PMP22')
markerGenePlot(proj, markSchwann)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba294f8b23-Date-2022-04-11_Time-12-30-46.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:30:46 : Plotting Embedding 1 2 3 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba294f8b23-Date-2022-04-11_Time-12-30-46.log
# from https://www.abcam.com/neuroscience/schwann-cell-markers-and-functions
# DNM2: https://elifesciences.org/articles/42404
# sox2: https://pubmed.ncbi.nlm.nih.gov/25859851/
markSchwann_search = c('SOX10', 'SOX2','MBP', 'DNM2')
markerGenePlot(proj, markSchwann_search)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba3dc18ee9-Date-2022-04-11_Time-12-31-08.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-04-11 12:31:08 : Plotting Embedding 1 2 3 4 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba3dc18ee9-Date-2022-04-11_Time-12-31-08.log
### Initial labeling of cells
############################################
# using marker gene scores, give cluster names
remapClust <- c(
'C1'='OPC',
'C2'='Oligo',
'C3'='Oligo',
'C4'='Oligo',
'C5'='Oligo',
'C6'='Oligo',
'C7'='Drop', # check with BaDoi
'C8'='Astro',
'C9'='Astro',
'C10'='Astro',
'C11'='UNK', # check with BaDoi
'C12'='Mening',
'C13'='Mening',
'C14'='Mening',
'C15'='MICRO',
'C16'='MICRO',
'C17'='Drop', # check with BaDoi
'C18'='UNK', # check with BaDoi
'C19'='NEUR',
'C20'='NEUR',
'C21'='NEUR',
'C22'='NEUR',
'C23'='NEUR',
'C24'='NEUR',
'C25'='NEUR'
)
proj$Celltype1 <- mapLabels(proj$ClustersH230, newLabels = remapClust,
oldLabels = names(remapClust))
table(proj$Celltype1)
Astro Drop Mening MICRO NEUR Oligo OPC UNK 8983 1087 1925 6372 3819 19159 2088 396
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Celltype1", embedding = "UMAPH230")
p1
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-2d2ba68d1bba0-Date-2022-04-11_Time-12-34-20.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-2d2ba68d1bba0-Date-2022-04-11_Time-12-34-20.log
# drop the drop clusters, pull out the neuron cell types
ARCHDIR2=file.path(PROJDIR,'ArchR_Seal001_NEUR')
idxSample <- BiocGenerics::which(proj$Celltype1 %in% "NEUR")
table(proj$Celltype1[idxSample])
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj,
cells = cellsSample,
outputDirectory = ARCHDIR2,
force = TRUE
)
NEUR 3819
Copying ArchRProject to new outputDirectory : /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchR_Seal001_NEUR
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 7): Embeddings
Copying Other Files (2 of 7): IterativeLSI110
Copying Other Files (3 of 7): IterativeLSI150
Copying Other Files (4 of 7): IterativeLSI190
Copying Other Files (5 of 7): IterativeLSI230
Copying Other Files (6 of 7): IterativeLSI30
Copying Other Files (7 of 7): IterativeLSI70
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# drop the drop clusters, pull out the glia cell types
ARCHDIR2=file.path(PROJDIR,'ArchR_Seal001_Other')
idxSample <- BiocGenerics::which(proj$Celltype1 %ni% c('NEUR', 'Drop'))
table(proj$Celltype1[idxSample])
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj,
cells = cellsSample,
outputDirectory = ARCHDIR2,
force = TRUE
)
Astro Mening MICRO Oligo OPC UNK 8983 1925 6372 19159 2088 396
Copying ArchRProject to new outputDirectory : /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchR_Seal001_Other
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 7): Embeddings
Copying Other Files (2 of 7): IterativeLSI110
Copying Other Files (3 of 7): IterativeLSI150
Copying Other Files (4 of 7): IterativeLSI190
Copying Other Files (5 of 7): IterativeLSI230
Copying Other Files (6 of 7): IterativeLSI30
Copying Other Files (7 of 7): IterativeLSI70
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
proj = loadArchRProject(path = file.path(PROJDIR,'ArchR_Seal001_Other'))
proj
table(proj$Celltype1)
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchR_Seal001_Other samples(5): DH-1_SEA1346A1 DH-3_SEA1346A3 DH-4_SEA1346A4 DH-5_SEA1346A5 DH-2_SEA1346A2 sampleColData names(1): ArrowFiles cellColData names(27): Sample TSSEnrichment ... ClustersH230 Celltype1 numberOfCells(1): 38923 medianTSS(1): 24.878 medianFrags(1): 11824
Astro Mening MICRO Oligo OPC UNK 8983 1925 6372 19159 2088 396
proj = loadArchRProject(path = file.path(PROJDIR,'ArchR_Seal001_NEUR'))
proj
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchR_Seal001_NEUR samples(5): DH-1_SEA1346A1 DH-3_SEA1346A3 DH-4_SEA1346A4 DH-5_SEA1346A5 DH-2_SEA1346A2 sampleColData names(1): ArrowFiles cellColData names(27): Sample TSSEnrichment ... ClustersH230 Celltype1 numberOfCells(1): 3819 medianTSS(1): 19.259 medianFrags(1): 21271